French Academic Compound LibraryChimiothèque NationaleUGM Budapest – 28th may 2013 Philippe Jauffret and Kiet TranChimioth...
Chimiothèque NationaleOutline1- Introduction : French academic compound library2- Current information system : data model,...
Chimiothèque NationaleChimiothèque Nationale [CN]1- Consortium of academic chemical laboratories(40 labs participating)2- ...
Chimiothèque NationaleCN’s organization overviewnationaldatabaseRequeststreatmentlaboratorynationalserverbiologistlocal da...
Chimiothèque NationaleArchitecture of the information system(2005-2013)NationalSDF FileCFusion toolsChemaxonAdministration...
Simplified Data Model(IDBS-CN)Chimiothèque NationalestructuresubstancebatchLaboratorybasketOrderUserAccess LogHas structur...
Online query moduleChimiothèque Nationale7
Online query module-similarity searchChimiothèque Nationale8
Online query module-batch viewChimiothèque Nationale9
Instant Jchem -Storage and query data screeningChimiothèque Nationale10
Simplified Data Model(Chemaxon-CN)Chimiothèque NationalestructuresubstancebatchLaboratorybasketOrderUserAccess LogHas stru...
New web architecture(Chemaxon-CN)Chimiothèque Nationale12NationalSDF FileCFusion toolsChemaxonAdministration ServerAPACHE ...
New query by name(May 2013-…)Chimiothèque Nationale13
State of project and prospectsChimiothèque Nationale1- Data model (OK)2- Installation and configuration : Oracle Linux, Or...
DiscussionChimiothèque Nationale15
Marvin 03140315382D13 14 0 0 0 0 0 0 0 0999 V20002.2043 0.1758 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 01.4898 0.5883 0.0000 C 0 0 ...
Data Model of natural extractsChimiothèque NationaleorganismOrganism_part17
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EUGM 2013 - Anh Kiet Tran Minh (CNRS): French Academic Compound Library: the “Chimiothèque Nationale”

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Created in september 2003, the “Chimiothèque Nationale” (CN) – French Academic Compound Library – has for mission to federate collections of synthesis products, natural compounds and natural extracts available in French academic laboratories and to promote their scientific and industrial valorisation. Information concerning available molecules and extracts are contained in two databases (synthesis products, natural compounds and natural extracts), accessible through a web portal (http://www.chimiotheque-nationale.org/). The compounds database currently refers about 50,000 molecules coming from 30 French academic laboratories. The chemical compound database is built on Oracle database and IDBS tools (ActivityBase and ChemXtra). Chemaxon tools are also integrated in the CN information system : Marvin applet and calculator plugins. For several reasons (including software maintenance costs and evolutivity), we decided recently to evaluate the possibility to move to Chemaxon tools (Jchem, Jchem Cartridge and Standardizer). I will show you the present and future (expected) use of Chemaxon tools in the CN information system.

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Transcript of "EUGM 2013 - Anh Kiet Tran Minh (CNRS): French Academic Compound Library: the “Chimiothèque Nationale”"

  1. 1. French Academic Compound LibraryChimiothèque NationaleUGM Budapest – 28th may 2013 Philippe Jauffret and Kiet TranChimiothèque Nationale
  2. 2. Chimiothèque NationaleOutline1- Introduction : French academic compound library2- Current information system : data model, database, web architecture3- Why a new information system based on chemaxon tools?4- Prospects2
  3. 3. Chimiothèque NationaleChimiothèque Nationale [CN]1- Consortium of academic chemical laboratories(40 labs participating)2- Double aim : - preserve the French academic chemical patrimony- promote its biological evaluationKey dates: 2003 : launch of the project 2005 : opening of Information System(www.chimiotheque-nationale.org) 2007 : creation of a service Unit of CNRS 2010 : partner of EU-Openscreen projectRecent scientific results (2008-2011) 53.000 compounds  200 collaborative projects 15.000 natural extracts  200 validated hits 5% growth/year  100 publications 350 users (biologists)  8 licenced patents3
  4. 4. Chimiothèque NationaleCN’s organization overviewnationaldatabaseRequeststreatmentlaboratorynationalserverbiologistlocal databaseDiffusionData mergingCollaborationLegalvalidationGISmembersGISmembers4
  5. 5. Chimiothèque NationaleArchitecture of the information system(2005-2013)NationalSDF FileCFusion toolsChemaxonAdministration ServerAPACHE (https) + PHP+ SSHBackstage National ServerNational Database(ORACLEActivityBase + ChemXtra)WEB BrowserAdministration ClientSDFFileLocal LibraryDatabaseLocal ManagementIsis/Draw MarvinSketch MarvinSketchIsis/Base L-g Chimio IJC other…other…SecuredConnexionsWEB Browser+ Sketch (JME/Marvin)Query Client5
  6. 6. Simplified Data Model(IDBS-CN)Chimiothèque NationalestructuresubstancebatchLaboratorybasketOrderUserAccess LogHas structureIs inProvidesProvidesDirect toDirect toHas selectedor orderedHas orderedHas itemHasaccessed toStructure_ididbsmolfileSmilescodeMolecular_massDelete StatusSubstance_nat_idSubstance_local_idPackagingQuantityPurityNature_substanceDate_creationDate_updateDelete Statuslot_nat_idlot_local_idDelete StatusStructure descriptors:-LogP, HBD, HBA, Lipinsky (Chemaxon)- Herg, Mutagen (Isida) 6
  7. 7. Online query moduleChimiothèque Nationale7
  8. 8. Online query module-similarity searchChimiothèque Nationale8
  9. 9. Online query module-batch viewChimiothèque Nationale9
  10. 10. Instant Jchem -Storage and query data screeningChimiothèque Nationale10
  11. 11. Simplified Data Model(Chemaxon-CN)Chimiothèque NationalestructuresubstancebatchLaboratorybasketOrderUserAccess LogHas structureIs inProvidesProvidesDirect toDirect toHas selectedor orderedHas orderedHas itemHasaccessed toCd_idStructure_idcd_ smilesCd_molecular_massMolfileInchiDescriptorsDelete StatusSubstance_nat_idSubstance_local_idPackagingQuantityPurityNature_substanceDate_creationDate_updateDelete Statuslot_nat_idlot_local_idDelete StatusStructure descriptors:-LogP, HBD, HBA, Lipinsky (Chemaxon)- Herg, Mutagen (Isida)screeningIs tested11Why use Jchem?
  12. 12. New web architecture(Chemaxon-CN)Chimiothèque Nationale12NationalSDF FileCFusion toolsChemaxonAdministration ServerAPACHE (https) + PHP+ SSHBackstage National ServerNational Database(ORACLE +Jchem Cartridge)WEB BrowserAdministration ClientSDFFileLocal LibraryDatabaseLocal ManagementIsis/Draw MarvinSketch MarvinSketchIsis/Base L-g Chimio JChemBase other…other…SecuredConnexionsWEB Browser+ Sketch (Marvin)Query Client
  13. 13. New query by name(May 2013-…)Chimiothèque Nationale13
  14. 14. State of project and prospectsChimiothèque Nationale1- Data model (OK)2- Installation and configuration : Oracle Linux, Oracle, Jchem (OK)3- Compounds loading ( in progress)4- Query module5- Data merging6- Test7- End of 2013 … : launch of the new information system14
  15. 15. DiscussionChimiothèque Nationale15
  16. 16. Marvin 03140315382D13 14 0 0 0 0 0 0 0 0999 V20002.2043 0.1758 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 01.4898 0.5883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 01.4898 1.4133 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 00.7754 0.1758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 00.0609 0.5883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0-0.6536 0.1758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0-1.3680 0.5883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0-2.0825 0.1758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0-2.0825 -0.6492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0-1.3680 -1.0617 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0-0.6536 -0.6492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 00.0609 -1.0617 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 00.7754 -0.6492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 01 2 1 0 0 0 02 3 2 0 0 0 02 4 1 0 0 0 04 5 2 0 0 0 05 6 1 0 0 0 06 7 2 0 0 0 07 8 1 0 0 0 08 9 2 0 0 0 09 10 1 0 0 0 010 11 2 0 0 0 06 11 1 0 0 0 011 12 1 0 0 0 012 13 1 0 0 0 04 13 1 0 0 0 0M END >> <bulk> (1)3000> <plate> (1)lot1> <id_local> (1)LPS1877> <purity> (1)90$$$$Sdf File : the exchange fileChimiothèque NationaleMandatory fields Optional fields:-substance nature- purity analysis method- observations16
  17. 17. Data Model of natural extractsChimiothèque NationaleorganismOrganism_part17

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